feature,element,definition,examples
scale,,What is the scale of study at which the resource is used?,
,whole,In-tact whole brain level including various computational or non-invasive methods,"non-invasive imaging, in-tact brain studies, whole-brain circuitry, whole-brain spatiotemporal dynamics"
,regions,Regional level including anatomical boundaries and inter and intra regional connectivity,"function/region specific studies like visual, attention, prefrontal area, fiber tracking pathways, etc"
,cellular,"Neuron level including cell body composition and complexity of axons, dendrites and cell-to-cell interaction","neurons, cell bodies, dendrites, axons"
,macromol.,Chemical/molecular level including gene and protein interactions,"chemical reactions, molecular pathways, gene expression profiling, protein interactions, etc"
,all,All of the above,
species,,Primary animal model used by the resource,
,primates,,"human, monkey"
,rodents,,"rat, mice, etc"
,insects,,fly
,others,,"worm, zebrafish, birds, etc."
,mammals,,"cat, elephant, and all mammals"
,all,All of the above,
resource_type,,What type of neuroinformatics resource does this fall into?,
,software,Applying/supporting automation process that computes and analyzes various kinds of data related to the nervous system,"plug-in tools, algorithm-based analytical software, GPU-based super computer, application-based software, hub or repo of software resources"
,ontology & data mngmt.,Explicitly sharing & supporting the usage of standard formats and machine-readable ontologies that  describe the underlying data models.,"dictionaries, term definitions, corpora, data integration practices, formal languages, ontologies, data sharing, standard file formats, mapping of shared data,  domain specific search services, literature mining, Formalism for the Representation of Connectivity Structure"
,database,"Resources that have a formal schema design to organize data. This allows to browse, archive, and search the content in a structured manner through a specific set of variables.",a formal database that the resource uses at the backend
,topical portal,A focused group where a single problem is discussed and supported in a collaborative setting providing open-access to data and supporting tools,"wiki, sourceforge, single topic collaborative initiative, resources found via topical portal"
,instrumentation,Usually a high-throughput way of acquiring and/or analyzing data by using a combination of hardware and software,"microscopy setup for automated sectioning, prosthetic device that helps human condition, cloud computing servers, behavioral data collection apparatus"
,atlas,Providing a commonly usable reference template for mapping brain regions in a given species in 2D/3D spatial axes. Such atlases are usually digitally sharable.,"magnetic resonance microscopy (MRM) based atlas, neurotransporter atlas, tract-tracing data based atlas, gene-expression based atlas, talairach atlas"
measurement,,What are the quantitative measures that the resource is built upon or is used for?,
,anatomical,Study of shape and size related features at both micro and macro level structures,"histology, immunohistochemistry, neuronal morphology, stereotactic images, tract tracing pathways, probabilistic fiber tractography, anatomical connectivity, structural imaging, angiography data, any shape related measures"
,functional,"To identify and map observed dynamical changes onto known functional states of the brain systems. functional states can be derived thoeretically or empirically based on different data sets such as behavioral, physiological, developmental, etc. These experiments usually include data collected at different time points ranging from fractions of seconds to different developmental stages of the model organism.","behavioral measures like attention, speech recognition,etc, fMRI related data, Response Monitoring, Tensor Metric, Volumetric Analysis, Region of Interest, Registration, Resampling, Nonlinear, Surface Analysis, Temporal Convolution - Deconvolution, Hemodynamic Response, Image Display, Rendering, resting state dynamics, functional genomics, developmental stages, information model, visual system, language acquisition, time series data, neural networks, etc."
,physiological,"To identify dynamically changing spatiotemporal patterns at various levels (molecular, single cell, network, and in-tact brain) ranging from computational simulations of molecular pathways to electrical recordings from patch clamping to activity response measures from MR imaging and EEG traces.","electrophysiology, action potential propagation, field recordings, EEG/ERP waves, biophysical modeling, physiological changes from T1-weighted MR images, modeling of cellular pathways, optogenetics, photostimulation, any activity related measures"
,biochemical,To identify biochemical changes from assays such as gene expression profiling on mRNA and DNA. Usually this involves high-throughput procedures like microarrays.,"microarrays, PCR analysis"
,all,All of the above,
application,,What is the basic utility of the resource?,
,visualization,"Analyzing data through 2D or 3D visualization. Almost any kind of neuroscientific data can be visualized (e.g., microscopy, neuroimaging and physiology) as statistical plots, graphical rendering of functional relationships, virtual reality models, etc.","neuroimaging, neuromorphology, movies, graph visualization, brain atlases, microscopic imaging, SEM imaging, in situ hybridization imaging, electrophysiological data visualization, raster plots, spike traces, electron microscopy"
,data analysis,"Any computational, mathematical or statistical approaches that are used on different types of data for automated or large-scale analysis purposes.","neural circuit analysis, electrophysiological data analysis, quantitative and statistical analysis, data mining, text mining, spatiotemporal analysis"
,annotation,"Using/supporting existing ontologies for data annotation, search & integration, resource categorization and electronic lab notebook keeping.","lab note book, data annotation, resource categorization, dictionary, tutorial, experimental usage"
,modeling & simulation,Simulation of functionally equivalent models or biologically realistic models that provide testable and reproducible results,"mathematical modeling, simulations, neuron modeling, network modeling"
,neurotechnology,Neuroscience inspired technologies build brain-based devices by emulating one or more behavioral or computational aspects of the higher order brain functions. These technologies are often used in the spirit of improving or repairing brain functions or building smart machines.,"neurorobotics, neuromorphic engineering, neural engineering, BCI interfaces, prosthetics, bionic devices, Nintendo Wii Remote"
area_of_study,,"What is the main aim of the resource, how is it helping Neuroscience research? The resources are categorized based on what's known about the resource (e.g., from about pages of their websites)",
,neuroinformatics,"A specialized subfield that uses interdisciplinary approaches for organizing & integrating shared neuroscientific data for various purposes such as facilitating computational neuroscience, achieving high-throughput data processing, efficiency and standardization. However, all software resources need not necessarily belong to Neuroinformatics.","image registration, segmentation, reconstruction, filtering, computer vision, brain mapping and atlasing, connectomics, data mining, biomechanics, high throughput applications,  multiple software compatibilities, integrative tools that use databases and atlases as a medium to achieve primary functionality, parallel computing"
,cogn. & behav. neurosci.,"A study of understanding the neural substrates of underlying cognition and behavior. This includes neurophysiological experiments studying the cognitive, behavioral, psychological and decision making processes for supporting the development of clinical applications and/or brain computer interface devices.","neuropsychology, learning, movement tasks, speech imagery tasks, visual image reconstruction, wrist displacement, visual grating, virtual reality, etc."
,comput. neurosci.,A study of brain function using mathematical/computational approaches towards understanding the information processing mechanisms of various neural processes that constitute nervous system.,"network modeling and simulations, neuron modeling, mathematical/statistical modeling, study of neural circuits, visual system, systems biology at macromolecular level"
,neuroanatomy,Is a study of anatomy and organization of the nervous system at both micro and macroscopic levels.,"computational neuroanatomy, neuromorphology, subcellular anatomy, ultrastructural anatomy, ultra neuroimaging, microscopy imaging"
,clinical & dev. neurobiol.,Is an area that has high translational research potential in applying neuroscience research for clinical/medical purposes and for  studying of fundamental processes that govern normal brain development and function. This usually involves study of data at different time points.,"surgery aid, disease related information, medical data analysis, prosthetics, development neuroanatomy, developmental neurophysiology, transgenic animals, aging"
,"cell., mol., & syst. neurosci.","A study devoted to understanding the role of chemical and molecular composition and interactions that underlie cellular structure and function in conjunction with multi scale understanding of the brain systems. The systems neuroscience tries to understand the nervous system by applying the experimental data that describes the neuronal activity to build coherent computational models that explain how the different units interact with each other in a functional system such as vision, sensation, attention, etc.","molecular neuroanatomy, dendritic spines, neurogenesis, molecular signaling pathways, synaptic plasticity, genomics, neurophysiology, electrophysiology, neuromechanical modeling"
user_support,,How well are the resources documented for re-usability?,
,user manual,"Description about what, how and when to use the resource","documentation, description, tutorial"
,FAQs,Quick facts and questions,"quick facts, quick statistics, quick tour"
,user forum,A dedicated wiki system or user forum to support the users of the resource,"mailing list for users/developers/community, bug trackers, bitbucket"
,blog/social networking,"Links to blogs, facebook or twitter accounts for outreach activities",providing links to blogging/social networking sites
,citations,Books or publications that describe the usage of the resource,resources that have citations by the external users
resource_availability,,Sharing the source code or executable with the public,
,open source,"Source code, scripts, R programs, etc. are available for download","source code, scripts"
,freeware,Software is available for free use,free use
,licensed,Available for purchase,commercial